GEO DataSets

(Submitter supplied) Gut-on-chip devices enable exposure of cells to a continuous flow of culture medium, inducing shear stresses and could thus better recapitulate the in vivo human intestinal environment in an in vitro epithelial model compared to static culture methods. We aimed to study if dynamic culture conditions affect the gene expression of Caco-2 cells cultured statically or dynamically in a gut-on-chip device and how these gene expression patterns compared to that of intestinal segments in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17692

8 Samples

Download data: CEL

(Submitter supplied) The multifunctional intestinal mucus layer plays a crucial role in human health. Our understanding of the human colonic mucus layer in terms of structure, function and has been largely dependent on expensive and advanced ex vivo or in vitro models, which often require high expertise. The mucus-producing intestinal cell line HT29-MTX-E12 has been commonly used in more simple in vitro models, but produces only low amounts of the intestine-specific MUC2. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17692

15 Samples

Download data: CEL

(Submitter supplied) Due to the widespread application of food-relevant inorganic nanomaterials, the gastrointestinal tract is potentially exposed to these materials. Gut-on-chip in vitro model systems are proposed for the investigation of compound toxicity as they better recapitulate the in vivo human intestinal environment than static models, due to the added shear stresses associated with the flow of medium in line with what cells experience in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17692

31 Samples

Download data: CEL

(Submitter supplied) goal of this study was A) to compare global RNA-sequencing (RNA-seq) profiles data of organoid- derived colonic epithelial cells cultured and differentiated in i) conventional suspension organoids cultures (n=3), ii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and stretch (n=4), iii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and with stretch (n=4), iv) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and without stretch (n=4), v) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and stretch (n=6), vi) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and stretch (n=4), vii) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and with stretch (n=4), viii) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and without stretch (n=4), ix) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and stretch (n=3), and B) to identify differences in transcriptome profiles of organoid- derived colonic epithelial cells between following two conditions, unstimulated and basolaterally stimulated with IL-22 (10pM, 100pM or 1nM) Colon Intestine-Chips.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

48 Samples

Download data: CSV

(Submitter supplied) Orally administered drugs are absorbed and metabolized in the intestine. In order to accurately predict pharmacokinetics in the intestine, it is essential to understand the intestinal expression profiles of genes related to drug absorption, distribution, metabolism, and excretion (ADME). However, in many previous studies, gene expression analysis in the intestine has been carried out using specimens from cancer patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

33 Samples

Download data: XLSX

(Submitter supplied) Necrotizing enterocolitis is an intestinal disease induces rapid destruction of the epithelial monolayer of the neonatal intestine. Clinically relevant models of this disease are lacking. Using our novel microfluidic model of necrotizing enterocolitis, we characterized the response of intestinal epithelial cell-derived organoids to intestinal bacteria isolated from a neonate with fatal NEC. We subsequently used RNA-sequencing to determine the gene expression profile of these cells after 24 or 72 hours of incubation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: XLSX

(Submitter supplied) A human gut-on-a-chip microdevice was used to coculture multiple commensal microbes in contact with living human intestinal epithelial cells for more than a week in vitro and to analyze how gut microbiome, inflammatory cells, and peristalsis-associated mechanical deformations independently contribute to intestinal bacterial overgrowth and inflammation. This in vitro model replicated results from past animal and human studies, including demonstration that probiotic and antibiotic therapies can suppress villus injury induced by pathogenic bacteria. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

6 Samples

Download data: CEL, CHP

(Submitter supplied) Changes in cell adhesion molecule (CAM) expression and miRNAs regulating them are known to be involved in malignant progression in colon cancer. We investigated expression profiles of CAM genes and non-coding RNAs in CaCo2 colon cancer cells in static culture and under dynamic flow conditions perfused in microfluidic chip emulating physiological microenvironment. We incubated monolayers of CaCo2 cells in Transwell® units either under static conditions or under flow in a microfluidic chip. more...

Organism:

synthetic construct; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by array

Platforms:

GPL21572 GPL6244

12 Samples

Download data: CEL, CHP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL16027

72 Samples

Download data: TXT

(Submitter supplied) This is an experiment to study the effects of total body irradiation on intestinal gene expression. There are 24 male animals in the study; 4 controls, 10 animals received 6.7 Gy, 10 received 7.4 Gy. Animals were killed 4, 7 or 12 days after irradiation

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL16027

24 Samples

Download data: TXT

(Submitter supplied) This is an experiment to study the effects of total body irradiation on intestinal gene expression. There are 24 male animals in the study; 4 controls, 10 animals received 6.7 Gy, 10 received 7.4 Gy. Animals were killed 4, 7 or 12 days after irradiation

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL16027

24 Samples

Download data: TXT

(Submitter supplied) This is an experiment to study the effects of total body irradiation on intestinal gene expression. There are 24 male animals in the study; 4 controls, 10 animals received 6.7 Gy, 10 received 7.4 Gy. Animals were killed 4, 7 or 12 days after irradiation

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL16027

24 Samples

Download data: TXT

(Submitter supplied) The microphysiological human gut-on-a-chip has demonstrated in vivo-relevant cellular fidelity of intestinal epithelium compared to its cultures in a static condition1, 2. Microfluidic control of morphogen gradients and mechanical cues robustly induced morphological histogenesis with villi-like three-dimensional (3D) microarchitecture, lineage-associated cytodifferentiation, and physiological functions of a human intestinal Caco-2 epithelium3, 4. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: TAR

(Submitter supplied) Custom array chip focusing on transporters and ion channels. Genes are represented by 70 mers.

Organism:

Homo sapiens

1 DataSet

1 Series

32 Samples

Download data

(Submitter supplied) Intestinal epithelial stem cells (ISCs) are the focus of recent intense study. Current in vitro models rely on supplementation with the Wnt agonist R-spondin1 to support robust growth, ISC self-renewal, and differentiation. Intestinal subepithelial myofibroblasts (ISEMFs) are important supportive cells within the ISC niche. We hypothesized that co-culture with ISEMF enhances the growth of ISCs in vitro and allows for their successful in vivo implantation and engraftment. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: TXT

(Submitter supplied) Identification of cellular functions and signalling pathways of intestinal epithelial cells modulated by enteric glial cells Keywords: Transcriptome regulation

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8798

20 Samples

Download data: GPR

(Submitter supplied) The molecular interactions between the maternal environment and the developing embryo that are key for early pregnancy success are known to be influenced by factors such as maternal metabolic status. Our understanding of the mechanism(s) through which these individual nutritional stressors alter endometrial function and the in utero environment for early pregnancy success is, however, limited. Here we report, for the first time, the use of an endometrium-on-a-chip microfluidics approach to produce a multi-cellular endometrium in vitro, that was exposed to glucose and insulin concentrations associated with maternal metabolic stressors. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

30 Samples

Download data: TXT

(Submitter supplied) Molecular adaptation of the intestinal mucosa occurs during microbial conventionalization to maintain a balanced immune response. However, the genetic regulation of such adaptation is obscure. Here, combined analysis of germ free and conventionalized mice revealed that the major molecular adaptations were initiated at day 4 of conventionalization with a strong induction of innate immune functions followed by stimulation of adaptive immune functions. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4319

Platform:

GPL11533

144 Samples

Download data: CEL

Temporal analysis of colon, ileum, and jejunum from conventionalized males (i.e., germfree mice colonized with total fecal microbiota of their conventionally born and raised siblings). Results provide insight into molecular basis of innate and adaptive immune responses during conventionalization.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 protocol, 7 time, 3 tissue sets

Platform:

GPL11533

Series:

GSE32513

144 Samples

Download data: CEL

(Submitter supplied) Objective: The purpose of this study is to describe colonic cells differential transcriptomes and cellular pathways directly modulated by exposure to prebiotics. Prebiotic oligosaccharides are widely used as animal and human in-feed additives for their beneficial effects on the probiotic gut microbiota. A number of studies have revealed a protective effect of several oligosaccharides on dysfunctional or challenged intestinal cells models through microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT